tSNP: A dimensionality reduction algorithm for genetic data

Rethinking human AMY1 copy number evolution in light of demographic history

Strong bottlenecks constrain adaptive evolution in a host–parasite metapopulation

Fine-scale genotyping reveals assemblage-wide introgression in ants

Deep-Time History of Balkan Brown Bears

Local genomic adaptation to rabies in raccoons

From Core to Periphery: Mapping Evolutionary Potential Across Species Ranges

Positive Selection Across Scales: Genetic Architecture of Adaptation and Connectivity in Wild Sunflowers

Massive genetic diversity loss within Asian elephant subspecies: new insights for determining conservation priorities

The genomic basis and evolution of maternal genetic effects on early -life immunity in Soay sheep

Assessing dog introgression through structural variants in European refugial wolf populations

Genomic signatures of recent inbreeding are associated with rarity and habitat specialisation among flies of the UK.

Is genetic differentiation between species homogeneous across mammals?

Effects of habitat arrangement on gene flow and genetic diversity in a grassland-specialist butterfly (Cupido minimus)

Adaptive evolution under extreme genetic erosion in invasive Spotted Lanternfly

Gene expression and disease susceptibility of the genetically depauperate Channel Island fox (Urocyon littoralis)

Understanding the roles of Endozoicomonas in marine animals: Mutualists, parasites, and everything in between?

Streptococcus amylase-binding proteins in geladas and baboons reveal convergent oral microbial adaptation to starch-rich diets in humans and primates

Holo-omic insights into host–microbiome dynamics during starvation and compensatory growth in zebrafish

Leveraging large-scale long-read sequencing data to understand the diversity, drivers and evolution of Lepidoptera cobionts at unprecedented resolution

Zooming into Host–Microbiome Evolution via Micro-Scale Spatial Metagenomics

What lives in, on, and around a lichen?

The New Zealand Butterfish - A model teleost to understand holobiome interactions

The role of Wolbachia in reproductive isolation and speciation in Drosophila paulistorum

Metagenome-derived population genomics of a vertically transmitted endosymbiont during ecological speciation of its insect host

Disentangling the relationships between microbial taxa and metabolic outputs in a seaweed holobiont

Ecology and evolution of the mammalian oral microbiome elucidated using museum specimen metagenomics

Beyond the Constant: Structural, Life-History, and Environmental Drivers of Germline Mutation Rate Variation

Trinucleotide genome composition reflects context-dependent mutation spectra in plants

Transcription, Replication, and Recombination Shape Local Mutation and Sequence Variation at Human TSSs

Beyond Molecular Error: Developmental Selection Biases Germline Mutation Rates

A Statistical Framework for Mutation Model Inference of Tandem Repeat Variants via the Ancestral Recombination Graph

Are Triallelic SNPs generated by trans-lesion synthesis?

Germline mutation rate variation and its consequences for speciation in a cichlid adaptive radiation

Heritability of germline mutagenesis in 40 large three- and four- generation pedigrees

The mutational processes in primate spermatogenesis inferred from HiFi long read sequencing

Spontaneous mutation rate and spectrum are modulated by organismal fitness

Transcription start sites experience a high influx of heritable variants fueled by early development

Predicting interaction partners and generating protein sequences using protein language models

Molecular evolutionary analyses with protein foundation models from deep learning

Combining agentic AI with open infrastructure for reproducible analyses

Adaptive Phylogenetic Tree Search via Machine Learning-Based Parameter Selection

Likelihood-free inference of phylogenetic tree posterior distributions

Molecular phylogenetics directly from deep learning protein foundation models

plAIgue: An Artificial Intelligence Framework for Detecting Microbial Species in Ancient Human DNA

TKF-based models with latent and hierarchical structure are competitive with parameter-heavy neural networks as models of protein sequence evolution

Scaling and Representation Learning for Deep Ancestral Sequence Reconstruction

Improved Power to Detect Sparse Episodic Positive Selection:A Protein Language Model-Informed Branch-Site Approach

Phylogenetic regression of sequence embeddings reveals genotypic basis of phenotypes

Machine Learning Reveals Path-Dependent Functional Evolution in Animal Opsins

Self-organizing map as a new AI algorithm for motif characterization

Fatal entanglement: how a DNA satellite causes reproductive isolation in Drosophila

The tdk family: an evolutionarily persistent single-gene killer meiotic driver family employing a toxin–antidote strategy

Dissecting the genetic basis of the Paris SR meiotic drive system in Drosophila simulans

To purge or not to purge? How mating systems shape transposable element dynamics in Mimulus (monkeyflowers)

An ancient allele directs epigenetic suppression of a selfish reproductive barrier in maize

A large selfish mitochondrial deletion hints at an unexpected diversity of drive strategies

Nondisjunction and fitness costs in a selfish X chromosome that causes meiotic drive in both sexes in Drosophila testacea

Natural variation in sex chromosome drive enables the discovery of a neo-X meiotic drive gene family

Epistasis between gene expression noise and functional mutations shapes cellular fitness

Insertion of an invading retrovirus regulates a novel color trait in swordtail fish

Extensive Reorganization of the Escherichia coli Chromosome Over 75,000 Generations of Laboratory Evolution

Evolutionary history of two X chromosome meiotic drivers and polymorphic Y chromosomes in Drosophila affinis

Convergent genome evolution shaped the emergence of terrestrial animals

Recovering Lost Kveik Diversity in Farmhouse Brewing with Ancient Metagenomics

Intraspecific variation in the duration of epigenetic inheritance

The origins and molecular evolution of sperm

Evolution of a Diving Response: Divergent Transcriptomic Adaptations in Aquatic Versus Terrestrial Mammals.

The Vertebrate Genomes Project Phase I: A global reference genome resource

Comparative Population Genomics of Two Pipefish Species in the Baltic Sea

Comparative genomics reveals chemosensory gene family evolution within a conserved genome architecture in Culex

A deep-learning-based score to evaluate multiple sequence alignments

Using petabase-scale sequence alignment to describe the host and phylogenetic diversity of microsporidian parasites

CMAPLE 2: High-Performance Phylogenetic Inference for Millions of Pathogen Genomes

New genome assemblies from neglected phyla illuminate the evolution of Ecdysozoa

Testing the adequacy and the accuracy of models of amino-acid substitution across evolutionary timescales

An updated perspective: what genes make a tree a tree?

A macroevolutionary gene network reveals diapause evolutionary dynamics beyond the circadian clock and predicts microevolution

The Toll-like receptor signalling pathway repertoire of cartilaginous fishes: loss of TLR4-LPS signalling as a case study

Tripling known fungal mitogenomes through large-scale public data reuse

Genome characterization of rainbow trout-associated Midichloria-like organism reveals a novel, potentially pathogenic bacterial lineage in a vertebrate host

Cellular Innovation through De Novo Gene Birth Driven by Promiscuous Protein–Protein Interactions

Devils, Disease and Defence: the immune system strikes back

Understanding the evolutionary dynamics of host and pathogen through comparative transcriptomics

Divergent cis-regulatory haplotypes at Tlr2 are associated with immune responsiveness

Evolutionary diversification of horizontally acquired pathogen- defence genes in bdelloid rotifers

VIEWING IMMUNITY IN THE CONTEXT OF AGEING AND EVOLUTION

Evolutionary Signatures of Host–Pathogen Interactions Revealed by Polygenic Adaptation in Ancient Genomes

The evolutionary dynamics between viral mimics and host proteinss14

The population-level mutation dynamics of SARS-CoV-2 spike under immune selection

Intraspecific diversity shapes functional variability of bats innate immunity

The specialist – generalist trade-off for infection ability of a parasite

Integrating protein structure and population genomic data to detect diversifying selection related to immunity

Evolutionary rescue under extreme selection: Linking adaptation and demography in agricultural weeds

Genomic and Phenotypic Differentiation of Cydia pomonella Populations Under Varied Pest Management Regimes in France

Unwanted evolutionary rescue: bidirectional adaptive introgression of pesticide resistance genes between native and invasive Helicoverpa crop pests

Convergent and divergent genetic routes to persistence under thermal stress in the yeast genus Saccharomyces

Cooperative interactions between measles viruses facilitate rapid dissemination throughout the brain

Evolution of genetic variance and genetic architecture in the context of species’ range dynamics

Occurrence and potential of inter- and intraspecific gene flow in rapidly adapting butterfly populations

The effects of environmental stress on the genetic architecture of fitness

Evolutionary rescue via short-lived modifiers of genetic variation

Paralog interference contributes to the preservation of genetic redundancy

The Gene Regulatory Evolution of the Human Skeleton

Mapping the Local Biochemical Landscapes of TEM-1 β-Lactamase

Cumulative epistatic changes in fitness effects drove contingency and entrenchment in the billion-year evolution of Hsp90

Bacterial dynamics of evolution tracked by barcodes over 20,000 generations validate a century of theoretical models of adaptation

Parsing nearly neutral theory at the protein level through experimental variation of effective population size and high- throughput biophysical measurements

Tracking the evolution of protein fusion entrenchment via genomic directed evolution

Assessing Growth–Survival Trade-offs in Fluctuating Environments

Experimental reconstruction of the domestication, evolution, and adaptive role of horizontal gene transfer in eukaryotes.

Understanding the rules of regulation: Rewiring gene networks with synthetic regulators from random sequence

Interplay of gene conversion and nucleotide skews is driving the evolution of macrolide antibiotics

Leveraging public data for comparative evolutionary genomics of arthropod biodiversity

Rare variation in malaria parasites biases population-genetic inference

Integration and comparison of public single-cell RNA-Seq data for animals in the Bgee database and the scFAIR consortium

Completing the Tree of Life with High-throughput Phylogenetics

Expanding the Mammalverse of Genomes

Mining Public Metagenomic Archives Reveals Deep-Time Evolution and Hidden Diversity of the Human Oral Microbiome

FAIRness of polymorphism data matters for plant demographic inference

Developing open tools and datasets to uncover the role of whole genome duplications in early vertebrate evolution

RepeatOBserver: Tandem repeat visualisation and putative centromere detection in 2000 genomes from across the tree of life

What do bats and belugas have in common? Comparative genomics reveals convergent anti-deafness adaptations in echolocating Cetacea and Chiroptera

Understanding the diversity of adhesive proteins in sea stars (Echinodermata, Asteroidea)

Characterizing HIF-pathway alteration across two early diverging metazoan lineages (Ctenophora, Porifora).

Genomic fossils reveal hidden evolutionary processes underlying phylogenetic conflicts in avian radiations

Evolutionary dynamics of extinct and extant moose hybridization in North America

Paleolithic prevalence of human color vision diversity

Characterization of archaic ancestry in 63,000 Japanese individuals from the Tohoku Medical Megabank

Functional characterization of archaic introgression reveals immune system adaptation in Near Oceania

Pleistocene wolves genome revealed new insight on migration and hybridization in North American canids

Ancient DNA from birch tar artefacts: insights into population structure and gendered practices in Neolithic Alpine Europe

The Green Sahara genomic landscape: tracing ancestries across North Africa and Sahel through joint analysis of modern and ancient genomes

Gene regulatory signatures of archaic introgression across human tissues and cell types

Archaic Introgression in ancient Eurasians

Multiple Denisovan lineages shaped the genomic diversity of Asian populations

The Evolution of HLA Diversity in a Native American Population from Ancient to Modern Times

An archaeogenomic study of Black Death victims from Southern Europe

Signals of hybridization between commercial and wild bumblebees revealed by temporal genomics

Ancient DNA and functional genomics retrace the path to modern chicken productivity

ratePlacer: A Phylogenetic Framework for Molecular Dating of Ancient Environmental DNA

Paleogenomics Reveals Arctic Range and Aquatic Specialization in the American "cheetah", Miracinonyx trumani

Genetic load, drift debt, and the evolutionary management of vulnerable populations

Genomic diversity across 200 plant species of variable Red List status

A practical framework for identifying genetic subpopulations and ESUs: insights for IUCN assessments and broader management

Genera: An Integrative AI Framework for Conservation Management using Comparative Genomics at Scale

Functional genomic diversity and migratory survival: implications for evolutionary management of a critically endangered parrot

Genomic Consequences of Translocations: Lessons from the Critically Endangered Pyrenean Brown Bear

Assessing adaptive potential in Scandinavian populations of Willow ptarmigan (Lagopus lagopus) using temporal genomics

Harnessing genetic rescue: from genomic evidence to management decisions

Detecting Vulnerability Early: Genomic Signals from Fragmented Landscapes

Costs and benefits of genetic rescue of the critically endangered helmeted honeyeater from another subspecies

Environmental effects on the origin and establishment of Arabidopsis arenosa

Exploring Tree Space: Exact Transition Kernels and Proposal Efficiency in Bayesian Phylogenetics

Disentangling Ghost and Reciprocal Introgression in Four-Taxon Genomic Datasets

Detecting balancing selection using ancestral recombination graphs

A New Technique for Ultra-Fast Maximum Likelihood That Gives Exact Phylogenetic Gradients for Free

HOGPROP: transferring functional annotation and reconstructing ancestral function

Representing massive-scale phylogenetic uncertainty with phylogenetic networks

The multi-species ancestral recombination graph reveals admixture dynamics in a hybrid baboon population

The application of ancestral recombination graphs to understand the temporal dynamics of hybridization

Powerful inference of bacterial evolution from genome-wide genealogies

What drives genome expansions in the fungal kingdom? From populations to deep timescales

An in-vivo approach to population 3D genomics: age and sex affect 3D genome in a healthy controlled cohort of chickens.

Beyond the textbook centromere: genome evolution across monocentric–holocentric transitions in Drosera

An increase in chromosome copy number drives rapid adaptation in a cold-adapted bacterium

Genome plasticity through a large chromosomal inversion structures phenotypic and regulatory responses to environmental variation

Chromosomal loss trajectories following whole-genome duplication in cancer

An epigenetically induced hypermutator state reshapes genome architecture through elevated structural variation

Copy That: Exceptional Retrocopy Abundance in Sloths and Xenarthrans

A theoretical perspective on the two-speed genome model

Construction of unbiased pangenomes to better characterize standing variation and structural rearrangements between closely related butterfly morphs

Alu-associated structural variation contributes to species-specific differences in genome organization across primate evolution

Primary cilia regulation linked to evolution of sex determination in vertebrates with and without sex chromosomess

Drivers of primary sex ratio bias in dwarf willow

Bagworm moths: a new model for studies of genome evolution across variable levels of sexual dimorphism, from mild to extreme.

A comparison of selection on autosomes and the young Xchromosome in diploid Mercurialis species

Diversity of dosage compensation mechanisms in squamate reptiles

Convergent evolution of genetic sex determination among species of stickleback fishes

A Tale of Skink Sex Chromosome Evolution

Causes and consequences of sex-chromosome turnovers in Diptera

Evolution of recent autosomic translocations to the X of iconic neotropical bats

Alternative splicing and sex-specific adaptation in stick insects

Evolution of immunity across domains of life

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes

Dissecting the factors underlying sequence evolution by disentangled representation learning

Mapping bacterial capsule diversity using protein structural homology

Deciphering and forecasting viral evolution via AI-augmented molecular evolution

Genomic Language Models for DNA sequence Analysis

A random forest classifier to retrieve Insertion Sequences carrying antibiotic resistance genes from wastewater samples.

StrataBionn: a neural network supervised classification method for microbial communities

LLM Reveals: Viruses Copy Synonymous Cell-Type Specific Patterns of Human Coding DNA

Parallel Molecular Evolution Across Replicated Anolis Lizard Adaptive Radiations

The genomic underpinning of variation in vision across a global sample of ant workers

The day after the drug: Investigating drug-induced cellular memory

A fast-evolving C-terminus underlies species-specific function of an orphan gene required for sperm nuclear shaping

Functional characterization of the male-specific mitochondrial ORFan protein in DUI bivalves reveals a role in spermatogenesis

Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions

Crossover and consequences: are individual recombination rates under selection?

Disentangling patterns of variation in the human genome: the rolesof mutation, recombination and selection revisited

What sets the upper bound on animal cell size?

Frequency-dependent immune selection in tumors inferred from neoantigen depletion patterns

Haplotype specific structural variation within a single human genome

The origin and evolution of alkaloid sequestration in poison frogs

Genomic Plasticity and Evolutionary Innovation in Avian Metabolic Adaptation

A Blast from the Past: ‘Living Fossil’ Fish Genomes Bridge Gene Regulation Across Long Evolutionary Distances

Tandem repeat variation is functional with signatures for directional and balancing selection in humans and chimpanzees

Profiling mutation rates and characteristics of somatic structural variants in the aging brain using long read sequencing

Genomic legacy of near extinction and intensive management in the pink pigeon

Phenotypic plasticity shapes genetic variation and patterns of inbreeding and extinction risk

Pedigree‑based analysis reveals rapid de novo insertion and purging of retroviral integrations in the koala genome

Parallel adaptation and genomic vulnerability of bottlenose dolphins in a changing ocean

When Social Structure Shapes Genomes: Modeling Demography and Genomic Signals in Reef Fishes

Tracing the Genomic History of Spotted Owls and Their Relatives

Persistence and Resilience: Tracking the Genomes of North American Brown Bears

The genomic consequences of introgression for an island-limited rail

Leveraging standardised frameworks for genetic monitoring of populations

Predicting Mammal-Wide Variant Pathogenicity, Uncertainty, Gene Essentiality, and Genetic Load

Investigating Parallel Adaptation to Altitude and Response to Climate Change in Neotropical Butterflies

Restoring Vulnerable Populations via Genomic Rescue

Using population structure and admixture analyses to inform management decisions of native caribou in Greenland

Structural variant load under demographic change: How a small fly can provide big insights

Population Genomics of the Rice’s Whale Reveals Long-term Isolation, Admixture, and Genetic Distinctiveness

Heterosis vs. adaptation: genomic insights from a 25-year mixed- source plant translocation program

Biological Sequence Language Models for Prediction and Design

From Likelihood to Fitness: Accounting for Phylogeny to Improve Variant Effect Prediction

Learning protein interaction origination and evolution with sequence- based machine learning

From Sequence to Expression Across Evolution: Promise and Limits of AI Genome Models

Nonlinearity in Complex Trait Genomics: Limits of Linear GWAS and Interpretable Deep Learning for Locus Discovery

A new genomic foundation model and a sequence-only gene prediction model for plant evolutionary biology

Functional impact prediction for single nucleotide variants in Drosophila melanogaster with FlyCADD

Comparing archaic and modern human genomes using deleteriousness predictions from a DNA language model

The Evolutionary Ecology of Color Vision in Krill: Comparative Genomics, Machine Learning and Analysis of Standing Genetic Variation in Opsins

Macro-evolutionary perspectives on a large chromosomal rearrangement underlying alternative life-histories in seaweed flies

Mobile chromosomes as drivers of clonal pathogen evolution

Transposable Elements in Ant Macroevolution

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods

The contribution of epigenetic regulation to antimicrobial resistance phenotypes in Escherichia coli from antibiotic-free dairy farms

Programmed DNA elimination as a source of genomic plasticity in free-living nematodes

Extensive sex chromosome rearrangements in cichlid fish

When plasmids settle down: domestication and chromid-like evolution in Pantoea

Structural variants and their contribution to successful and unsuccessful colonizations

Telomere-Specific Transposable Elements and Host Fitness in Drosophila

Modeling the Evolutionary Advantage of Plasmid Persistence Strategies

Genome-Wide Association Analysis reveals insights into Escherichia coli adaptation to specific clinical niches

Transposable element islands at the interface of 3D genome architecture and karyotype evolution in ants

Exploring architectural diversity in fungal 3D genomes to uncover new perspectives on eukaryotic chromatin organization

Long-read sequencing reveals the genomic architecture of alternative reproductive tactics in swordtail fishes

From Sterility to Clonality: Linking Rapid Sex-Chromosome Turnover to Asexual Reproduction in a Vertebrate Hybrid Complex

Functional verification of a genetic trigger for female sex determination in the Marsabit clawed frog (Xenopus borealis)

Sex chromosome turnover: why some sex chromosomes never settle, and others never leave.

Sex-specific modifications of gametogenesis in natural and lab-bred Fundulus spp. hybrids

Reproductive morph specialisation facilitated by a maternal sex determining region in a fungus gnat (Bradysia coprophila)

Evolutionary and Functional Consequences of W–Autosome Fusions in Heliconius Butterflies

Repeated losses of self-fertility shaped heterozygosity and polyploidy in yeast evolution

Unveiling the Evolutionary Dynamics of the X Chromosome in Aphids

Sex chromosome variation across vertebrate genome assemblies

Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene

Tetrapolar mating relaxes host boundaries through sexual recombination between wheat- and barley-adapted Puccinia striiformis rust fungi.

Sex-chromosome evolution and speciation in the genus Salmo

Neo-sex chromosome evolution and reproductive isolation in hybridizing gazelle lineages

How and why genes survive on the human Y chromosome: Insights from telomere-to-telomere ape assemblies, long-read transcriptomes, and protein modeling

Experimental evidence that balancing selection maintains sexually antagonistic genetic variation in a polygenic trait

Sex chromosome turnover has dramatically different consequences between closely related cichlid fishes

Plant domestication under clonality and traditional management: perspectives from cassava collections

ANCIENT PLANT DNA DOCUMENTS CEREMONIAL CONTINUITY AT PICURIS PUEBLO

Following the process of sunflower domestication through space and time with ancient DNA

Two centuries of genetic diversity change in rice at different spatial scales

Tracking molecular mechanisms of plant adaptation to climate change with herbaria

Leveraging Herbarium Collections to access Natural Genetic Variation

Historical Genomes Reveal a Centuries-Long Competition–Colonization Trade-off in Plant-infecting Pseudomonas

A herbariomic approach to characterising medicinal black henbane (Hyoscyamus niger) populations in Britain

The phylogeography of the Wikstroemia genus – one phylogeny, 50 species, 60 islands, and 250 years of botany

Leveraging variation of matri- and patrilinear genomes reveals contrasting patterns of sex-bias dispersal in northern sea lions

Coalescent-Based Introgression Inference: Theory, Biases, and Solutions

ARG-based inference of regional maize demographic histories

Environmentally-driven asynchrony in genomic reconstructions of demographic responses to past climate change and human expansion across hundreds of bird populations

The detection of selective sweeps associated with adaptation to lead (Pb) contamination in wild house sparrows

Comprehensive Characterization of Inversions across the Human Population using Strand-seq Pooled and Long-Read Sequencing

From Drift Debt to Inbreeding Depression: Genomic Consequences of Population Decline in Ruffed Lemurs

The westward expansion of Asian rice

Landscape barriers shape genetic connectivity in the Golden langur (Trachypithecus geei)

Investigating the genomics of reindeer (Rangifer tarandus) domestication

Pangenomes Illuminate Genetic Diversity in Sheep and Their Wild Relatives

Genomic Insights into Biodiversity Decline in Endangered Hallig Beetle, Pseudaplemonus limonii

Evaluating GWAS Power Using SLiM Simulations in Structured Populations

Genetics of repeated ecotype separation in Malawi cichlid genus Labeotropheus

Adaptive introgression from Pacific to Atlantic herring facilitates rapid niche exploration in the Baltic Sea

Late Neandertals of North-Western Europe

Ancient DNA from Shimao city records kinship practices in Neolithic China

Introgression from an unsampled lineage in Southern African genomes

Characterising and timing the four independent Denisovan admixture events in Asia and Oceania

Genealogy-based analyses shows modern humans were formed through multiple deep admixtures

Evaluation of a target capture approach for plant dietary identification from paleofeces

Uncovering previously unrecognized gene flow from modern humans into Denisovans

Gene-culture coevolution in the European Upper Palaeolithic

Genomic Landscapes of Oceania and Island Southeast Asia: Insights from 92 populations

Deep-Time Demographic Inference in the Americas Using Site Frequency Spectrum–Based Modeling

Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples

The phylogeny of Archaea as a case study of challenges in reconstructing very deep evolutionary relationships

Reconstructing the origin of the genetic code

Ancient Reconstructed Proteins, inferring ancient proteins fromancient metagenomics samples

Comparative analysis of eukaryotic protein complex orthologs

Beyond conserved markers: enhancing deep node resolution via rigorous orthology filtering of 900 protein domains

NS-QMaker: Non-Stationary Amino-Acid Substitution Models Facilitate Deep Phylogenetic Inference

Eukaryote-like evolution of Asgard archaeal genomes

Reticulation dominates protein structural evolution in bacteriophages

Rooting the deep divergence of land plants

Exploring Time-Nonreversibility in Deep Phylogenetics with ABySS

FastSpeciesTree: Fast and Scalable Species tree Inference

Whole-genome sequencing of Black Death victims reveals an immune gene under natural selection

On Inferring the Virulence of Ancient Pathogens, Especially Prehistoric Plague

Ancient Genomic Analysis of a New Mycobacterium tuberculosis Lineage from Iron Age Britain

Bayesian approaches to root phylogenetic trees under root uncertainty: evaluation using empirical and simulated ancient and modern pathogen data

First ancient genome of Streptococcus pyogenes from a pre- Columbian Bolivian mummy reveals its presence in the Americas before European contact

Bacterial Disease and Viral Emergence in Holocene Hunter- Gatherers from Patagonia

Tracing the origin and evolution of early smallpox in South America

Insights from ancient DNA into deep-time evolution of oral microbes in the Cusco region of the Peruvian Andes

Ancient Treponema pallidum genomes reveal phylogenetic diversity and lineage persistence through time in South American populations

Co-isolation of ancient DNA and RNA from non-formalin-fixed lung specimens reveals host-pathogen interactions during the Industrial Revolution in Great Britain.

Identifying the presence of Yersinia pestis in Medieval Turkey during the Second Plague Pandemic

A deeply divergent Yersinia pestis lineage identified in Early Iron Age Romania

The deadly past of Yersinia enterocolitica: insights from paleogenomics

Genomic signatures of increasing disease burden in recent prehistory

Parvovirus B19 from early modern warships suggests genotype 2 continuity in Europe, bridging a millennium-long gap

Humans as reservoirs: Historical microbiomes uncover hidden zoonotic pathways

Diversity of recombination landscapes across taxa: from genetic control to genomic architecture

Rapidly Evolving Epigenetic Controlling Factors of Meiotic Recombination

Tuning meiosis in different habitats: lessons from Arabidopsis arenosa

Self-fertilization can reverse the selection coefficient on a recombination landscape modifier during experimental evolution

Heterogeneous evolution of effective recombination landscapes across percomorph fishes

A holocentric pangenome links karyotype evolution to meiotic recombination

Fine-scale mapping of meiotic recombination in Saccharomyces cerevisiae unveils shifts in genetic exchanges driven by DNA heterologies

Loci under balancing selection can change the recombination landscape around them

Turtles reveal novel insights into PRDM9’s role in recombination rate landscape evolution

From Foundations to Futures: Building Equity in Genetics

Introducing the IDEA taskforce

Science Wise: Career mentorship through a storytelling interview podcast

Can evolutionary studies on social traits promote 21st-century eugenics?

Navigating Tribal Collaboration in Environmental and Genomic Research in California

From Specimen to Sequence: International Researcher Perspectives on Indigenous Data Sovereignty in Biodiversity Genomics

EvoSur: Building an interconnected network for evolutionay biology in South America

Mapping JEDI Challenges in the Earth BioGenome Project

Biomedical and life science articles by female researchers spend longer under review

Project Psyche: A case study of how to embed inclusivity within large -scale genomic projects

Panel discussion

Efficient Bayesian Phylogenetics under the Infinite Sites Model

Comparative Genomics of Syngnathiform Fishes

Gene losses promoted skeletal innovation and cancer resistance in turtles

Ancestral introgression and the origin of a unique asexual vertebrate, the Amazon molly

Evolution of the inflammasome pathway in bats: a comparative genomics perspective

Rapid chromosome evolution in parthenogenetic Panagrolaimus nematodes

Evidence for asynchronous rediploidisation following the 1R whole genome duplication in vertebrates

Genome reorganisation in Ithomiini butterflies

A telomere atlas to study vertebrate chromosome evolution

Genetic and transcriptional signatures of evolutionary mismatch in the Orang Asli of Peninsular Malaysia

Root-symbiotic entomopathogenic fungi use distinct Pth11 G-protein coupled receptors for plant and insect recognition

New meiofaunal genomes reveal the diversity of animal Hox clusters

The genomics of miniature animals: the first genomes of the microscopic phyla Gnathostomulida and Micrognathozoa

Maintenance of net deleterious mutations in polymorphism in fluctuating environments

Genome size: Did flight loss relax genome size constraints in birds?

Regulatory Plasticity as an Adaptive Strategy in Malaria Parasites

Miniaturization – a major player in Metazoan Evolution

Balancing and Positive Selection Shapes the Spot Patterning Phenotype in the Masai Giraffe

Pervasive and convergent changes in the kynurenine pathway contribute to sugar-diet adaptations in bats

Mutation bias is a key predictor of adaptation rate

Somatic mutation genomics to elucidate longevity in the extremely long-lived desert plant Welwitschia mirabilis

SELECTED TO SHINE:ENZYMES REPURPOSED FOR BIOLUMINESCENCE IN BRITTLE STARS

Not one Y, but five: evidence for mixed origins of Y haplotypes across the common frog’s range

The Hidden Cost of Speed: A Molecular Conflict Between Light Damage and Visual Recovery in Human Evolution

Pollen tube competition is mediated by a gene subject to Positive Selection in Arabidopsis

An Exploratory Assessment of Opsins in Pleurobrachia pileus

Pervasive lateral gene transfer among grasses as a driver of metabolic innovation

Schistosoma mansoni single cell transcriptomics reveals recently duplicated genes specifically expressed in the host-parasite interfase.

Molecular principles of iridescent color formation in bird feathers

Trophic specialization drives contrasting evolutionary dynamics of chemosensory genes in blowflies

Non-coding RNA regulation in differentiating ZW sex chromosomes

Molecular mechanisms involved in homologous and intramolecular recombination in Coronaviruses

RESEARCH FUNDING OPPORTUNITIES WITH THE EUROPEAN RESEARCH COUNCIL

Highlights of ERC project and testimonial

Highlights of ERC project and testimonial

Q&A

Concerted evolution and unorthodox recombination of human subtelomeres

Population-scale genotyping from low-coverage sequencing using pangenome graphs

Multidimensional variation and population stratification across 8000 complete human centromeres

Population genetic analysis of G-quadruplexes across the human pangenome

A Baltic Cod pangenome for population inference

The Brassica super-pangenome uncovers novel exploitable genetic resources for crop breeding

The role of structural variants during adaptation to whole genome duplication

Inferring ancestral alleles and signatures of selection in cattle from a pangenome graph

Disentangling Reticulate Evolution in the Mediterranean Wall Lizards with a Super Pangenome

Pangenome-based investigation of genomic diversity in Kaolinonychus: A harvestmen lineage with deep admixture history and troglophilic adaptation (Arachnida, Opiliones, Paranonychidae)

Pangenome analyses for understanding adaptation to ash dieback disease in European ash populations

A pangenomic approach to evaluate fate of ancesteral and novel structural variants in a homopoloid hybrid sparrow.

Is my population locally adapted? Establishing the influence of natural selection in the real world.

Disentangling drift and selection in an endangered plant using temporal genomics and language models

Disentangling background selection from associative overdominance in structured populations using gene trees

Detecting local adaptation within chromosomal inversions

Parallel genomic adaptation promoting replicate range shifts of the blue-tailed damselfly, Ischnura elegans, in Scotland and Fennoscandia

Detecting local adaptation to biotic and abiotic environmental conditions in the cosmopolitan ectomycorrhizal fungus Cenococcum geophilum

The genomic architecture of rapid local adaptation under extreme demographic perturbations in native and invasive cichlid fish populations

Genomic time-series of a butterfly biocontrol agent reveal selection under extreme demographic constraint

Early Interferon Pathways as Targets of Selection in an Anthropogenic Yellow Fever - Primate System

Signals of positive selection on transposable element control genes across structured human populations

No evidence for recent selection on amylase copy number in humans

Understanding the rate of somatic mutations and epimutations in trees

Leveraging contemporary genotype-environment associations to predict maladaptation in pecan natural populations

A Landscape Genomic story of the olive tree in the western Mediterranean : insights into local adaptation and future (mal-) adaptation

Characterizing the DNA methylation landscape in O. sativa ssp indica

Investigating Effects of Inversions and Recombination Modifiers to Ecotypic Differentiation in Wild Sunflowers

Genome diversification and polyploidy in under-utilised, climate resilient millet crops in the grass genus Digitaria

Predicting Fitness in Future Climates: A Proof of Concept in Arabidopsis thaliana and Vitis vinifera subsp. sylvestris

Genomic signal of local adaptation in UK silver birch (Betula pendula)

Genomic analysis reveals local adaptation and vulnerability to climate change of the African orphan crop finger millet (Eleusine coracana)

A cross-linking enzyme underlies the development of feather structural coloration in birds

One Hundred Years of West Nile Virus Envelope Protein Adaptation

Single-cell analysis of prefrontal cortex differences in selectively bred tame and aggressive foxes (Vulpes vulpes)

Diverse Genomic Routes to the Same Protein: Evolutionary Mechanisms of New Gene Birth and Molecular Convergence

Deciphering Ion-Dependence of Fitness Effects of Protein Mutations

Identifying noncoding contributions to life history evolution with machine learning

Evolution of mutation rate in a simulation system with an explicit genome representation and a complex genotype-to-phenotype map

Convergent molecular evolution of thermal tolerance in mammals

Evolutionary consequences of recombination suppression: the case of a chromosomal inversion in the seaweed fly

Selection on sexual chromosomes and circadian genes during speciation in two Amazonian butterflies

Public microbial single-cell RNA sequencing data reveal opposing transcriptional relationships at population and single-cell scales

Quantifying DNA Methylation Consistency and Specificity Across Genomes

Quantifying the Genome-Wide Effect of Polygenic Selection over a Single Generation

Multi-Omics Characterization of the Hibernation Phenotype in Ground Squirrels

Gene-by-gene evolution of dosage compensation in a neo-XY sex chromosome system

The genomic basis of hostplant usage in a rapidly radiating clade

Using museomics to track the domestication of insects reared for feed and food

Palaeogenomics and the multiverse of elephant ivory trade

Paleogenomics and habitat modeling reveal temperate Eurasian origins of Late Quaternary woolly rhinoceroses

Metagenomic Characterization of Canids from the Pre-Contact (3,475–360 yBP) Patagonian Coastal Region of Argentina

Ancient DNA Reveals Millennia of Morphological Stability Despite Climate-Induced Gene Flow in European Crows

Museum specimens characterize natural repertoire of antimicrobial resistance inwildlife and reveal human impact of antibiotic use.

Pathogen-Host Genomic Interactions as Drivers of Invasion Success

Ancient-modern genomes reveal an impact-dependent erosion of functional diversity in Atlantic bluefin tuna

A preliminary look into the paleogenomics of Anatolian big cats

Reconstructing the genomic history of Ice Age grey wolves

Comet, a genome from the dawn of cattle breeding

Neglected microbial lineages and the birth of eukaryotic protein domains: A structural phylogenetics perspective

Patterns of molecular evolution across prokaryotes

Plant terrestrialization: evolutionarily conserved mechanisms in UV acclimation in the closest algal relatives of land plants

BLInG: Enabling Genomic Studies of Unicellular Organisms to Illuminate Major Evolutionary Transitions with Single-cell Genomics

Diversity and integration of endosymbiotic associations in microbial eukaryotes

Multilevel drift and selection in the evolution of prokaryotic plasmid

Evidence supporting a viral origin of the mitosing nucleus

Epigenetics in Archaea: Chromosome conformation underlies heritable resistance to oxidative stress in Sulfolobus islandicus

Spatial proteomics reveals lipid droplet reorganization in symbiotic Paramecium bursaria cells

An independent phylogenomic dataset sheds new light on the eukaryotic Tree of Life

Diversity of the protist world and the origin of animal multicellularity

Investigating cell type-specific gene expression in Salpingoeca rosetta

The evolution of new vertebrate cell types and organs

Evolutionary conservation and rewiring of enhancer-promoter connectivity across mammals

Cross-species chromatin accessibility maps reveal regulatory drivers of mammalian lifespan evolution

A multi-omics approach to unravel the evolution of gene regulation in vertebrates

Coevolution of microRNAs and their gene targets leads to novel traits – insights from across the vertebrate tree of life.

A dog is not a wolf – how tiny differences have shaped man's best friend

Ancient Epigenetic Insights into Woolly Mammoth Adaptations

Cis and trans contributions to cell type–specific regulatory evolution in primates

An Evolutionary Multi-Omic Framework to Assess the Evidence for Adaptive Regulatory Evolution Across Diverse Molecular Traits

A statistical framework for DNA methylation repeatability in natural populations

Cell-Autonomous Adaptations in High-Altitude Human Populations

170 million years of Y chromosome evolution

The functional impact of adaptive variants in South Asian populations

Increased survival of low-frequency lineages during fluctuations in resource abundance

Origin and host diversification of giant viruses infecting eukaryotes

A simulation framework for the study of population-level processes in phylogenetics

The evolution of exceptionally low mutation rates in plant mitochondrial and plastid genomes

Giant toxin genes, extreme genome variation, and repeated hybridization in harmful bloom-forming haptophyte golden algae

You Don’t Know What You’ve got ‘Til It’s Gone: Using non-biting mosquitoes to understand the evolution of blood-feeding.

Functional analysis of proteins encoded in mammalian endogenous parvovirus

Transposable Element Co-Option Drives Transcription Factor Neofunctionalization.

Ancient Epstein-Barr virus genomes from Mesolithic and Neolithic birch tar reveal early viral diversity and immune escape

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes.

Characterizing tumor-specific human endogenous retroviruses in clear cell Renal Cell Carcinoma patients

Recovery of an 18th Century Rhinovirus Genome through Ancient RNA Isolation of Human Lungs

Co-option of long terminal repeats mediates endogenous retrovirus dysregulation in cancer

Tracing the spread of Beak and Feather Disease Virus over the past two centuries

Comparative analysis of KAP1 binding reveals species-specific KRAB-ZNF regulatory landscapes in primates

Comparison of Methods for the Capture of Virus Genomes Using Formalin-Fixed Paraffin-Embedded Tissues

Novel examples of natural selection in ethnically and culturally diverse sub-Saharan Africans

Farming termites and microbial symbiont: enzymes and natural products in an evolutionary ecology context

Ancestral sequence reconstruction reveals simple genetic mechanisms for evolving octocoral bioluminescence

Germline-specific patterns of hypomethylation of previously inaccessible regions of ape genomes

Is sex-biased expression an evolutionary advantage – or a liability?

Epigenetic variation of Y-chromosome palindromic regions across human populations revealed by nanopore sequencing

Homologous recombination in stationary phase bacteria

Genomic reconstruction of the bacterial toolkit for plastic biodegradation

Ancient microRNAs Reveal Regulatory Continuity in a 41,000-Year- Old Insect

Hologenomic signatures of Arctic adaptation in Greenland sled dogs

Hybrid zones and a deadly fungus: adaptive selection and microbiomes in Bombina toads

Between fidelity and flexibility: host-specialist and generalist Helicobacter in Podarcis lizards

From post-glacial to the Anthropocene: the adaptation landscape dynamics of arthropod species in Denmark

Ancient HLA Variation and Predicted Immune Responses During Epidemics in Colonial Mexico

Genome compartmentalization in a fungal insect pathogen reveals a second mating-type locus on an accessory chromosome

Different mutation rates, shared architecture: SNPs and SVs across the Neurospora crassa interactome

Molecular Insights into the Burmese Python Invasion of the Florida Everglades

Ecology-mediated demographic instability shapes genetic diversity in a cichlid adaptive radiation

Using genomics to predict inbreeding depression risk: Case studies in Hawaiian birds

Two decades of yellow-bellied marmot population sampling reveals physiological and regulatory resilience to the metabolic costs of seasonal climate change

Biodiversity genomics research practices require harmonising to meet stakeholder needs in conservation

Genomic consequences of population collapse and recovery in European wolves

Four centuries of commercial whaling eroded 11,000 years of population stability in bowhead whales

Combining environmental DNA with nuclear loci capture for genetic monitoring of endangered butterfly populations

Whole genome resequencing enables temporal reconstruction of purifying selection in a highly bottlenecked avian population

How informative is demographic inference from genomic data for conservation?

The frontier of genome SFS-based demographic inference

Modeling repeats allows k-mer-based, alignment-freemethods to calculate population genomic distances

High genomic connectivity and climate-linked demographic decline in the snowy owl

Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea‐Level Fluctuations

Mechanistic fitness landscapes in random metabolic networks: from epistatic to ecological interactions

Mapping the immunity-dependent fitness seascape of influenza

Molecular mechanisms of gene regulatory evolution revealed by in vivo genotype–phenotype maps

Inference of high-dimensional fitness landscapes with site-specific contributions to epistatic interactions

The shifting nature of the SARS-CoV-2 fitness landscape

Temperature-Dependent Biochemical Landscapes of TEM-1 β- Lactamase

Modelling the genetic control of phenotypic stochasticity in genotype- phenotype-fitness maps

Indels in genotype-phenotype maps cannot simply be ignored because of their low rate

Epistasis informed protein fitness landscapes improve evolutionary modelling in bacterial genomes

Building realistic genotype-phenotype-fitness maps that predict mutant fitness in diverse environments

The regulation of evolutionarily new genes

Mechanisms for how cis-regulatory elements arise from transposable elements illustrated by repeated domestication in snake venom genes

Polygenic traits adaptation leads to selection of beneficial alleles in local regulatory hubs

How DNA methylation changes shaped recent human evolution

Evolution of dominance modifiers over 16 million years

Consistent signatures of selection on gene expression level at different evolutionary scales

RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions

Comparative inference of regulatory mechanisms driving age‑related splicing changes across vertebrate species

Measuring selection on regulatory networks combining population transcriptomics and experimental evolution

Transcriptional Reprogramming as a Primary Driver of Long-Term Cold Adaptation in Wild Yeast

Identifying phenotype- and tissue-associated regulatory elements across species using public genomic and transcriptomic data

Salmonids reveal principles of regulatory evolution following autotetraploidization

Investigating gene regulatory underpinnings of human-great ape divergence: insights from new models

Decoding gene essentiality from cross-species transcriptional constraints

Evolutionarily dynamic enhancer transcription links chromatin regulation to drought response in rice (Oryza sativa)

Gene expression variation underlying local adaptation in silver birch (Betula pendula)

Bacterial ecospecies: extraordinary new models for studying complex adaption.

Modeling regulatory evolution under the assumption of local oligogenicity

Tracing Protein Fold throughout Evolution using Synthetic Biology and Protein Design

Volcanic drivers of human demographic collapse and genetic divergence on New Britain Island

Convergent Evolution in Tumor Genomes Targets Functional Domains from Ancient to Lineage-Specific

Transposable element exaptation as a source of novel genes in polyploid wheat evolution

Competition, compensation and inbreeding depression in the evolution of conifer polyembryony

Bayesian test of gene flow between sister lineages using genomic data

Socially Responsive Paleoproteomics: Scientific Advances, Challenges, and Ethical Pathways in African Hominin Research

Characterisation of a male Neanderthal from Prado Vargas, Spain, via enamel paleoproteomics

Time to rethink how to analyse ancient collagen

Reconstructing the pre-Anthropocene evolutionary history of right whales

Evaluating protein preservation in dental calculus from natural history specimens for dietary reconstruction

Gene editing livestock for sustainable agriculture

Potential for alleviating inbreeding depression using gene editing

Engineering Hope: How Genetic Rescue Biotechnologies are Reshaping Wildlife Conservation

Evaluating the efficiency of captive genetic rescue versus genome editing of ancestral variation

ARIA's Accelerating Adaptation programme: Engineering Resilience in a Changing World

The trans-Pacific voyage that shaped the pattern of genetic variation and enrichment of functional alleles in Native Hawaiians

Collapse, recovery and future uncertainty: temporal genomics and simulations of genomic erosion in the Mauritius kestrel

Population boom or bust? Kraken the population connectivity and demographic history of Octopus vulgaris

Heavy-tailed dispersal and its impact on local adaptation: Revisiting the British peppered moth

Repeatable genomic responses to climate during global invasion

Eco-evolutionary drivers of the emergence of the major wildlife pathogen, Ranavirus

Population history and migration in sub-Saharan African Drosophila melanogaster

Comparing population genomic variation across ploidy levels

The origins of domestic sheep and wool production in the Nordic Bronze Age

Have arctic wolves adapted to the arctic environment?

Whole-Genome Population Genomics Reveals Lineage Structure and Adaptive Potential of Philaenus spumarius, the Principal Vector of Xylella fastidiosa in Europe

Thriving against the odds: bottlenecked invaders show evidence for purging

Spatial and temporal patterns of genetic variation in Northern European pedunculate oak populations

Genome association studies of range-wide introduction of Douglas fir in Europe

Population and Gene Flow Decline Following Landscape Fragmentation and it's Consequences for Genetic Load in Soil Arthropods

Palaeogenomic insights into late Quaternary African faunas

Introduction

DAFNEE: a database of academia-friendly eco-evo journals to facilitate transitioning towards responsible publishing.

Where to Publish? Building a database of for-profit and non-profit journals in life sciences.

The Tie That Binds Us? Challenging the Primacy of DNA in Kinship Studies and Re-Centering Community in Defining Human Connections

Stay in your lane: developing effective approaches to multidisciplinary research and publishing to address twenty first century challenges.

Scientist as a citizen-subject in a collapsing habitat

SMBE Present Awards

Final words from SMBE 2026

SMBE 2027